# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:55:55 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCc2c(C1)n(CC(=O)N[C@H](Cc3ccccc3)C(O)=O)c4ccc(Br)cc24
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2VD  2VD  '(2R)-6-bromo-9-(2-{[(1R)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid'  ligand  55  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2VD
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2VD  CAM  C   CH2   0  -0.514   3.2854  -2.8289  -0.1408
 2VD  CAL  C   CH2   0  -0.450   2.5345  -4.0065   0.4793
 2VD  CAK  C   CH1   0  -0.404   1.0270  -3.9198   0.1743
 2VD  CBD  C   C     0   0.575   0.3140  -5.1822   0.5934
 2VD  OBF  O   OH1   0  -0.594   0.6824  -6.2235  -0.1436
 2VD  OBE  O   O     0  -0.437  -0.4930  -5.2622   1.4862
 2VD  CAJ  C   CH2   0  -0.520   0.4003  -2.6901   0.8317
 2VD  CAH  C   CR5   0   0.353   1.2698  -1.5124   0.5693
 2VD  CAI  C   CR5   0  -0.030   2.5602  -1.5542   0.1309
 2VD  CAE  C   CR56  0   0.050   2.9952  -0.1988   0.0148
 2VD  CAF  C   CR16  0  -0.354   4.1969   0.3942  -0.3797
 2VD  CAA  C   CR6   0  -0.123   4.2674   1.7728  -0.3760
 2VD  BR   BR  BR    0  -0.073   5.8812   2.6140  -0.9081
 2VD  CAB  C   CR16  0  -0.259   3.1877   2.5805   0.0039
 2VD  CAC  C   CR16  0  -0.310   1.9939   2.0032   0.3977
 2VD  CAD  C   CR56  0   0.368   1.9085   0.6157   0.4050
 2VD  NAG  N   NR5   0  -0.590   0.8769  -0.2086   0.7629
 2VD  CAO  C   CH2   0  -0.483  -0.4495   0.2030   1.1049
 2VD  CAP  C   C     0   0.555  -1.3683   0.1728  -0.1105
 2VD  OAQ  O   O     0  -0.464  -0.9408   0.3008  -1.2422
 2VD  N    N   NH1   0  -0.633  -2.6720   0.0266   0.1785
 2VD  CA   C   CH1   0  -0.181  -3.6575  -0.0996  -0.8571
 2VD  C    C   C     0   0.550  -3.5500  -1.4620  -1.5304
 2VD  OXT  O   OH1   0  -0.590  -4.2350  -1.4890  -2.6633
 2VD  O    O   O     0  -0.421  -2.9438  -2.3992  -1.0824
 2VD  CB   C   CH2   0  -0.566  -5.0679   0.1031  -0.2802
 2VD  CG   C   CR6   0   0.152  -5.2314   1.4735   0.3172
 2VD  CD1  C   CR16  0  -0.300  -5.3517   2.5892  -0.5093
 2VD  CE1  C   CR16  0  -0.239  -5.4823   3.8604   0.0301
 2VD  CZ   C   CR16  0  -0.269  -5.4954   4.0353   1.4091
 2VD  CE2  C   CR16  0  -0.239  -5.3798   2.9305   2.2407
 2VD  CD2  C   CR16  0  -0.324  -5.2477   1.6588   1.6958
 2VD  H1   H   HCH2  0   0.248   4.3013  -2.7917   0.2606
 2VD  H2   H   HCH2  0   0.240   3.3923  -2.9878  -1.2192
 2VD  H3   H   HCH2  0   0.258   2.9481  -4.9398   0.0972
 2VD  H4   H   HCH2  0   0.243   2.6771  -4.0097   1.5637
 2VD  H5   H   HCH1  0   0.290   0.9141  -3.8329  -0.9128
 2VD  H6   H   HOH1  0   0.481   0.2242  -7.0227   0.1570
 2VD  H7   H   HCH2  0   0.270  -0.6102  -2.5353   0.4416
 2VD  H8   H   HCH2  0   0.268   0.2932  -2.8446   1.9101
 2VD  H9   H   HCR6  0   0.264   5.0400  -0.2147  -0.6803
 2VD  H10  H   HCR6  0   0.272   3.2760   3.6583  -0.0108
 2VD  H11  H   HCR6  0   0.272   1.1600   2.6315   0.6840
 2VD  H12  H   HCH2  0   0.301  -0.8390  -0.4197   1.9125
 2VD  H13  H   HCH2  0   0.323  -0.4231   1.2216   1.4978
 2VD  H14  H   HNH1  0   0.408  -2.9344  -0.2253   1.1188
 2VD  H15  H   HCH1  0   0.303  -3.4800   0.6675  -1.6153
 2VD  H16  H   HOH1  0   0.487  -4.2024  -2.3735  -3.0584
 2VD  H17  H   HCH2  0   0.289  -5.7951  -0.0431  -1.0799
 2VD  H18  H   HCH2  0   0.276  -5.2654  -0.6646   0.4725
 2VD  H19  H   HCR6  0   0.252  -5.3501   2.4630  -1.5861
 2VD  H20  H   HCR6  0   0.257  -5.5784   4.7153  -0.6267
 2VD  H21  H   HCR6  0   0.256  -5.6003   5.0267   1.8309
 2VD  H22  H   HCR6  0   0.257  -5.3929   3.0554   3.3158
 2VD  H23  H   HCR6  0   0.252  -5.1673   0.8015   2.3543

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2VD  CZ   CE1  aromatic  1.390  0.020  1.390
 2VD  CZ   CE2  aromatic  1.388  0.020  1.388
 2VD  CE1  CD1  aromatic  1.387  0.020  1.387
 2VD  CE2  CD2  aromatic  1.390  0.020  1.390
 2VD  OAQ  CAP  double    1.217  0.020  1.217
 2VD  CD1  CG   aromatic  1.394  0.020  1.394
 2VD  CAO  CAP  single    1.524  0.020  1.524
 2VD  CAO  NAG  single    1.430  0.020  1.430
 2VD  CD2  CG   aromatic  1.391  0.020  1.391
 2VD  CAP  N    single    1.343  0.020  1.343
 2VD  CAC  CAB  aromatic  1.383  0.020  1.383
 2VD  CAC  CAD  aromatic  1.390  0.020  1.390
 2VD  CG   CB   single    1.504  0.020  1.504
 2VD  NAG  CAD  aromatic  1.368  0.020  1.368
 2VD  NAG  CAH  aromatic  1.375  0.020  1.375
 2VD  CAB  CAA  aromatic  1.401  0.020  1.401
 2VD  CAD  CAE  aromatic  1.413  0.020  1.413
 2VD  N    CA   single    1.435  0.020  1.435
 2VD  CAH  CAJ  single    1.487  0.020  1.487
 2VD  CAH  CAI  aromatic  1.364  0.020  1.364
 2VD  CAJ  CAK  single    1.529  0.020  1.529
 2VD  CA   CB   single    1.537  0.020  1.537
 2VD  CA   C    single    1.523  0.020  1.523
 2VD  CAA  CAF  aromatic  1.380  0.020  1.380
 2VD  CAA  BR   single    1.896  0.020  1.896
 2VD  CAE  CAI  aromatic  1.428  0.020  1.428
 2VD  CAE  CAF  aromatic  1.397  0.020  1.397
 2VD  CAI  CAM  single    1.491  0.020  1.491
 2VD  CAK  CBD  single    1.509  0.020  1.509
 2VD  CAK  CAL  single    1.540  0.020  1.540
 2VD  OBE  CBD  double    1.206  0.020  1.206
 2VD  CBD  OBF  single    1.328  0.020  1.328
 2VD  C    O    double    1.203  0.020  1.203
 2VD  C    OXT  single    1.324  0.020  1.324
 2VD  CAM  CAL  single    1.528  0.020  1.528
 2VD  CAM  H1   single    0.970  0.020  1.090
 2VD  CAM  H2   single    0.970  0.020  1.090
 2VD  CAL  H3   single    0.970  0.020  1.090
 2VD  CAL  H4   single    0.970  0.020  1.090
 2VD  CAK  H5   single    0.970  0.020  1.090
 2VD  OBF  H6   single    0.850  0.020  0.980
 2VD  CAJ  H7   single    0.970  0.020  1.090
 2VD  CAJ  H8   single    0.970  0.020  1.090
 2VD  CAF  H9   single    0.930  0.020  1.080
 2VD  CAB  H10  single    0.930  0.020  1.080
 2VD  CAC  H11  single    0.930  0.020  1.080
 2VD  CAO  H12  single    0.970  0.020  1.090
 2VD  CAO  H13  single    0.970  0.020  1.090
 2VD  N    H14  single    0.860  0.020  1.020
 2VD  CA   H15  single    0.970  0.020  1.090
 2VD  OXT  H16  single    0.850  0.020  0.980
 2VD  CB   H17  single    0.970  0.020  1.090
 2VD  CB   H18  single    0.970  0.020  1.090
 2VD  CD1  H19  single    0.930  0.020  1.080
 2VD  CE1  H20  single    0.930  0.020  1.080
 2VD  CZ   H21  single    0.930  0.020  1.080
 2VD  CE2  H22  single    0.930  0.020  1.080
 2VD  CD2  H23  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 2VD  H2   CAM  H1   106.01  3.000
 2VD  H2   CAM  CAI  110.54  3.000
 2VD  H1   CAM  CAI  110.85  3.000
 2VD  H2   CAM  CAL  109.61  3.000
 2VD  H1   CAM  CAL  109.51  3.000
 2VD  CAI  CAM  CAL  110.23  3.000
 2VD  H4   CAL  H3   107.18  3.000
 2VD  H4   CAL  CAK  108.91  3.000
 2VD  H3   CAL  CAK  110.50  3.000
 2VD  H4   CAL  CAM  109.90  3.000
 2VD  H3   CAL  CAM  109.34  3.000
 2VD  CAK  CAL  CAM  110.93  3.000
 2VD  H5   CAK  CAJ  108.69  3.000
 2VD  H5   CAK  CBD  107.04  3.000
 2VD  CAJ  CAK  CBD  111.09  3.000
 2VD  H5   CAK  CAL  107.55  3.000
 2VD  CBD  CAK  CAL  111.11  3.000
 2VD  CAJ  CAK  CAL  111.18  3.000
 2VD  OBE  CBD  OBF  122.99  3.000
 2VD  OBF  CBD  CAK  111.76  3.000
 2VD  OBE  CBD  CAK  125.25  3.000
 2VD  H6   OBF  CBD  110.08  3.000
 2VD  H8   CAJ  H7   106.32  3.000
 2VD  H8   CAJ  CAH  110.05  3.000
 2VD  H7   CAJ  CAH  111.41  3.000
 2VD  H8   CAJ  CAK  110.50  3.000
 2VD  H7   CAJ  CAK  109.82  3.000
 2VD  CAH  CAJ  CAK  108.75  3.000
 2VD  NAG  CAH  CAI  110.16  3.000
 2VD  CAI  CAH  CAJ  125.85  3.000
 2VD  NAG  CAH  CAJ  123.98  3.000
 2VD  CAE  CAI  CAH  106.57  3.000
 2VD  CAE  CAI  CAM  130.40  3.000
 2VD  CAH  CAI  CAM  123.03  3.000
 2VD  CAD  CAE  CAF  119.66  3.000
 2VD  CAF  CAE  CAI  133.46  3.000
 2VD  CAD  CAE  CAI  106.88  3.000
 2VD  H9   CAF  CAA  121.51  3.000
 2VD  H9   CAF  CAE  120.64  3.000
 2VD  CAA  CAF  CAE  117.85  3.000
 2VD  CAB  CAA  BR   118.45  3.000
 2VD  BR   CAA  CAF  119.06  3.000
 2VD  CAB  CAA  CAF  122.49  3.000
 2VD  H10  CAB  CAC  119.36  3.000
 2VD  H10  CAB  CAA  120.53  3.000
 2VD  CAC  CAB  CAA  120.12  3.000
 2VD  H11  CAC  CAD  122.04  3.000
 2VD  H11  CAC  CAB  119.86  3.000
 2VD  CAD  CAC  CAB  118.10  3.000
 2VD  NAG  CAD  CAC  130.47  3.000
 2VD  NAG  CAD  CAE  107.74  3.000
 2VD  CAC  CAD  CAE  121.78  3.000
 2VD  CAO  NAG  CAD  126.05  3.000
 2VD  CAD  NAG  CAH  108.60  3.000
 2VD  CAO  NAG  CAH  124.84  3.000
 2VD  H13  CAO  H12  105.93  3.000
 2VD  H13  CAO  CAP  108.66  3.000
 2VD  H12  CAO  CAP  111.32  3.000
 2VD  H13  CAO  NAG  109.39  3.000
 2VD  H12  CAO  NAG  110.09  3.000
 2VD  CAP  CAO  NAG  111.27  3.000
 2VD  N    CAP  OAQ  123.55  3.000
 2VD  N    CAP  CAO  114.57  3.000
 2VD  OAQ  CAP  CAO  121.87  3.000
 2VD  H14  N    CA   118.19  3.000
 2VD  H14  N    CAP  118.71  3.000
 2VD  CA   N    CAP  121.38  3.000
 2VD  H15  CA   CB   108.47  3.000
 2VD  H15  CA   C    108.03  3.000
 2VD  CB   CA   C    110.40  3.000
 2VD  H15  CA   N    109.11  3.000
 2VD  C    CA   N    110.43  3.000
 2VD  CB   CA   N    110.34  3.000
 2VD  O    C    OXT  124.30  3.000
 2VD  OXT  C    CA   111.09  3.000
 2VD  O    C    CA   124.60  3.000
 2VD  H16  OXT  C    110.48  3.000
 2VD  H18  CB   H17  106.87  3.000
 2VD  H18  CB   CG   110.29  3.000
 2VD  H17  CB   CG   109.93  3.000
 2VD  H18  CB   CA   109.37  3.000
 2VD  H17  CB   CA   108.59  3.000
 2VD  CG   CB   CA   111.65  3.000
 2VD  CD2  CG   CD1  118.69  3.000
 2VD  CD2  CG   CB   121.08  3.000
 2VD  CD1  CG   CB   120.22  3.000
 2VD  H19  CD1  CE1  119.55  3.000
 2VD  H19  CD1  CG   119.71  3.000
 2VD  CE1  CD1  CG   120.74  3.000
 2VD  H20  CE1  CZ   120.12  3.000
 2VD  H20  CE1  CD1  119.75  3.000
 2VD  CZ   CE1  CD1  120.13  3.000
 2VD  H21  CZ   CE2  120.25  3.000
 2VD  H21  CZ   CE1  120.18  3.000
 2VD  CE2  CZ   CE1  119.57  3.000
 2VD  H22  CE2  CD2  119.74  3.000
 2VD  H22  CE2  CZ   120.16  3.000
 2VD  CD2  CE2  CZ   120.10  3.000
 2VD  H23  CD2  CE2  119.51  3.000
 2VD  H23  CD2  CG   119.73  3.000
 2VD  CE2  CD2  CG   120.76  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 2VD  CONST_01  CAC  CAD  NAG  CAH  180.00   0.0  0
 2VD  CONST_02  CAE  CAD  NAG  CAH    0.00   0.0  0
 2VD  CONST_03  CAD  CAE  CAI  CAH    0.00   0.0  0
 2VD  CONST_04  CAF  CAE  CAI  CAH  180.00   0.0  0
 2VD  CONST_05  CAD  NAG  CAH  CAI    0.00   0.0  0
 2VD  CONST_06  CAC  CAD  CAE  CAI  180.00   0.0  0
 2VD  CONST_07  NAG  CAD  CAE  CAI    0.00   0.0  0
 2VD  CONST_08  CAA  CAF  CAE  CAI  180.00   0.0  0
 2VD  CONST_09  CAB  CAC  CAD  CAE    0.00   0.0  0
 2VD  CONST_10  NAG  CAH  CAI  CAE    0.00   0.0  0
 2VD  CONST_11  CAB  CAA  CAF  CAE    0.00   0.0  0
 2VD  CONST_12  CAC  CAB  CAA  CAF    0.00   0.0  0
 2VD  CONST_13  CAC  CAD  CAE  CAF    0.00   0.0  0
 2VD  CONST_14  NAG  CAD  CAE  CAF  180.00   0.0  0
 2VD  CONST_15  CAD  CAC  CAB  CAA    0.00   0.0  0
 2VD  CONST_16  CAD  CAE  CAF  CAA    0.00   0.0  0
 2VD  CONST_17  NAG  CAD  CAC  CAB  180.00   0.0  0
 2VD  CONST_18  CZ   CE1  CD1  CG     0.00   0.0  0
 2VD  CONST_19  CZ   CE2  CD2  CG     0.00   0.0  0
 2VD  CONST_20  CE2  CZ   CE1  CD1    0.00   0.0  0
 2VD  CONST_21  CE2  CD2  CG   CD1    0.00   0.0  0
 2VD  CONST_22  CD2  CE2  CZ   CE1    0.00   0.0  0
 2VD  CONST_23  CD2  CG   CD1  CE1    0.00   0.0  0
 2VD  CONST_24  CAO  NAG  CAH  CAJ    0.00   0.0  0
 2VD  CONST_25  CAO  NAG  CAH  CAI  180.00   0.0  0
 2VD  CONST_26  CAO  NAG  CAD  CAE  180.00   0.0  0
 2VD  CONST_27  BR   CAA  CAF  CAE  180.00   0.0  0
 2VD  CONST_28  CAC  CAB  CAA  BR   180.00   0.0  0
 2VD  CONST_29  CAO  NAG  CAD  CAC    0.00   0.0  0
 2VD  CONST_30  CE1  CD1  CG   CB   180.00   0.0  0
 2VD  CONST_31  CE2  CD2  CG   CB   180.00   0.0  0
 2VD  CONST_32  H9   CAF  CAE  CAI    0.00   0.0  0
 2VD  CONST_33  H11  CAC  CAD  CAE  180.00   0.0  0
 2VD  CONST_34  H10  CAB  CAA  CAF  180.00   0.0  0
 2VD  CONST_35  H20  CE1  CD1  CG   180.00   0.0  0
 2VD  CONST_36  H22  CE2  CD2  CG   180.00   0.0  0
 2VD  CONST_37  H21  CZ   CE1  CD1  180.00   0.0  0
 2VD  CONST_38  H23  CD2  CG   CD1  180.00   0.0  0
 2VD  CONST_39  H19  CD1  CE1  CZ   180.00   0.0  0
 2VD  CONST_40  H6   OBF  CBD  CAK  180.00   0.0  0
 2VD  CONST_41  CA   N    CAP  CAO  180.00   0.0  0
 2VD  CONST_42  CA   N    CAP  OAQ    0.00   0.0  0
 2VD  CONST_43  H14  N    CAP  CAO    0.00   0.0  0
 2VD  CONST_44  H16  OXT  C    CA   180.00   0.0  0
 2VD  Var_01    CAH  CAI  CAM  CAL  -14.89  30.0  1
 2VD  Var_02    NAG  CAH  CAJ  CAK  165.57  30.0  1
 2VD  Var_03    CAI  CAM  CAL  CAK   45.77  30.0  1
 2VD  Var_04    CAP  CAO  NAG  CAH  -77.46  30.0  2
 2VD  Var_05    CD1  CG   CB   CA    73.84  30.0  2
 2VD  Var_06    OAQ  CAP  CAO  NAG  -26.29  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2VD  chir_01  CAK  CAJ  CBD  CAL  positiv
 2VD  chir_02  CA   N    CB   C    positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2VD  plan-1  CB   0.020
 2VD  plan-1  CG   0.020
 2VD  plan-1  CD1  0.020
 2VD  plan-1  CE1  0.020
 2VD  plan-1  CZ   0.020
 2VD  plan-1  CE2  0.020
 2VD  plan-1  CD2  0.020
 2VD  plan-1  H19  0.020
 2VD  plan-1  H20  0.020
 2VD  plan-1  H21  0.020
 2VD  plan-1  H22  0.020
 2VD  plan-1  H23  0.020
 2VD  plan-2  CAM  0.020
 2VD  plan-2  CAJ  0.020
 2VD  plan-2  CAH  0.020
 2VD  plan-2  CAI  0.020
 2VD  plan-2  CAE  0.020
 2VD  plan-2  CAF  0.020
 2VD  plan-2  CAA  0.020
 2VD  plan-2  BR   0.020
 2VD  plan-2  CAB  0.020
 2VD  plan-2  CAC  0.020
 2VD  plan-2  CAD  0.020
 2VD  plan-2  NAG  0.020
 2VD  plan-2  CAO  0.020
 2VD  plan-2  H9   0.020
 2VD  plan-2  H10  0.020
 2VD  plan-2  H11  0.020
 2VD  plan-3  CAO  0.020
 2VD  plan-3  CAP  0.020
 2VD  plan-3  OAQ  0.020
 2VD  plan-3  N    0.020
 2VD  plan-3  CA   0.020
 2VD  plan-3  H14  0.020
 2VD  plan-4  CAK  0.020
 2VD  plan-4  CBD  0.020
 2VD  plan-4  OBF  0.020
 2VD  plan-4  OBE  0.020
 2VD  plan-4  H6   0.020
 2VD  plan-5  CA   0.020
 2VD  plan-5  C    0.020
 2VD  plan-5  OXT  0.020
 2VD  plan-5  O    0.020
 2VD  plan-5  H16  0.020

